rs1748019

Variant names:

• chr1-17342481-G-C
• rs1748019
• NM_012387.3:c.935+79G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-17342481-G-C
• chr1-17342481-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012387.3(PADI4):​c.935+79G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0901 in 850,980 control chromosomes in the GnomAD database, including 3,807 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.098 (784 hom., cov: 32)
  • Exomes 𝑓: 0.088 (3023 hom.)
• Consequence: PADI4 NM_012387.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 7 publications found

Genes affected

PADI4 (HGNC:18368): (peptidyl arginine deiminase 4) This gene is a member of a gene family which encodes enzymes responsible for the conversion of arginine residues to citrulline residues. This gene may play a role in granulocyte and macrophage development leading to inflammation and immune response. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PADI4	NM_012387.3	c.935+79G>C		intron_variant	Intron 8 of 15	ENST00000375448.4	NP_036519.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PADI4	ENST00000375448.4	c.935+79G>C		intron_variant	Intron 8 of 15	1	NM_012387.3	ENSP00000364597.4

Frequencies

GnomAD3 genomes AF: 0.0975 AC: 14810 AN: 151938 Hom.: 777 Cov.: 32

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0562

Gnomad ASJ AF: 0.0588

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.0483

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0973

Gnomad OTH AF: 0.0845

GnomAD4 exome AF: 0.0884 AC: 61804 AN: 698922 Hom.: 3023 AF XY: 0.0863 AC XY: 31156 AN XY: 360912

African (AFR) AF: 0.121 AC: 2166 AN: 17936

American (AMR) AF: 0.0358 AC: 1020 AN: 28504

Ashkenazi Jewish (ASJ) AF: 0.0608 AC: 1006 AN: 16546

East Asian (EAS) AF: 0.0494 AC: 1675 AN: 33926

South Asian (SAS) AF: 0.0460 AC: 2707 AN: 58834

European-Finnish (FIN) AF: 0.109 AC: 5311 AN: 48812

Middle Eastern (MID) AF: 0.0377 AC: 149 AN: 3950

European-Non Finnish (NFE) AF: 0.0980 AC: 44722 AN: 456236

Other (OTH) AF: 0.0892 AC: 3048 AN: 34178

GnomAD4 genome AF: 0.0975 AC: 14831 AN: 152058 Hom.: 784 Cov.: 32 AF XY: 0.0968 AC XY: 7197 AN XY: 74340

African (AFR) AF: 0.126 AC: 5200 AN: 41426

American (AMR) AF: 0.0559 AC: 855 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0588 AC: 204 AN: 3468

East Asian (EAS) AF: 0.0490 AC: 254 AN: 5182

South Asian (SAS) AF: 0.0483 AC: 233 AN: 4824

European-Finnish (FIN) AF: 0.116 AC: 1227 AN: 10588

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0973 AC: 6615 AN: 67976

Other (OTH) AF: 0.0836 AC: 176 AN: 2106

Alfa AF: 0.0557 Hom.: 49

Bravo AF: 0.0935

Asia WGS AF: 0.0830 AC: 288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.53
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1748019; hg19: chr1-17668976;